title: Diversity and selective sweep in the OsAMT1;1 genomic region of rice.
abstract: BACKGROUND
  Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene OsAMT1;1 and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives.
  
  
  RESULTS
  Nucleotide polymorphism (Pi) of OsAMT1;1 was as low as 0.00004 in cultivated rice (Oryza sativa), only 2.3% of that in the common wild rice (O. rufipogon). A single dominant haplotype was fixed at the locus in O. sativa. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around OsAMT1;1 in O. sativa, but fell rapidly in O. rufipogon on either side of the promoter of OsAMT1;1, demonstrating a strong natural selection within or nearby the ammonium transporter.
  
  
  CONCLUSIONS
  The severe reduction in nucleotide variation at OsAMT1;1 in rice was caused by a selective sweep around OsAMT1;1, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely indica and japonica. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Zehong
authors.initials: Z
authors.lastname: Ding
authors.forename: Chongrong
authors.initials: C
authors.lastname: Wang
authors.forename: Sheng
authors.initials: S
authors.lastname: Chen
authors.forename: Sibin
authors.initials: S
authors.lastname: Yu
mesh_terms: D001483:Base Sequence; D027682:Cation Transport Proteins / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D012641:Selection, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D027682:Cation Transport Proteins; D018744:DNA, Plant; D010940:Plant Proteins; C088952:ammonium transporters, plant